1zgb

Crystal Structure of Torpedo Californica Acetylcholinesterase in Complex With an (R)-Tacrine-(10)-Hupyridone Inhibitor.
See also 1zgc and AChE bivalent inhibitors



The active site of Torpedo californica AChE (TcAChE, EC 3.1.1.7) is located at the bottom of a gorge which contains 14 conserved aromatic residues. This active site consists of two binding subsites. First is the "catalytic anionic site" (CAS), which involves 3 catalytic residues Ser200, His440, and Glu327 (colored orange) which hydrolyze the ester bond in acetylcholine (ACh). This subsite also includes the conserved residues Trp84 (colored magenta) and Phe330 (colored orange) which participate in ligands' recognition. Another conserved residue Trp279 (colored cyan) is situated at the second binding subsite, termed the "peripheral anionic site" (PAS), ~14 Å from CAS. Therefore, ligands which can interact with both these subsites simultaneously, are more potent AChE inhibitors in comparison to compounds interacting with CAS only. One of the ways to produce such ligands is to construct a compound with two reactive moieties. These moieties should be separated by an alkyl linker of suitable length. According to this strategy, the inhibitor (RS)-(±)-tacrine-(10)-hupyridone ((R)-3 or (S)-3) was designed and synthesized. It consists of tacrine (colored magenta ), 10-carbon linker (yellow), and hupyridone (red). The tacrine moiety of this inhibitor binds at the CAS, the linker spans the <scene name='1zgb/Act_site/12'>active-site gorge, and the hupyridone moiety binds at the PAS.

The comparison of the (R)-3/TcAChE and tacrine/TcAChE complexes at the <scene name='1zgb/Align/2'>active site. A <scene name='1zgb/Align/7'>comparison of the trigonal (R)-3/TcAChE structure (<font color='cyan'>(R)-3 colored cyan, TcAChE residues interacting with (R)-3 are colored sea-green) with the crystal structure of tacrine/TcAChE (1acj; <font color='magenta'>tacrine colored magenta ; residues interacting with tacrine are colored <font color='pink'>pink ) reveals a similar binding mode for the tacrine moiety. In both structures the tacrine ring is situated at the CAS, between the aromatic residues Trp84 and Phe330. Steric clash with the 10-carbon linker could explain the tilt observed for the Phe330 (yellow and transparent in the tacrine/TcAChE). <font color='red'>Water molecules are shown as red spheres. The tacrine unit of (R)-3 N forms <scene name='1zgb/Align/8'>hydrogen bond with His440 O (3.0 Å) similar to that of tacrine alone. Similarly to the tacrine/TcAChE structure the <font color='red'>system of three water molecules at the CAS ((R)-3/TcAChE) binds the tacrine-linker N via hydrogen bonds to Ser81 O, Ser122 Oγ, and Asn85 Oδ1 (2.6-3.5 Å).

The comparison of the (R)-3/TcAChE and hupyridone/TcAChE complexes (1h22 and 1h23) at the <scene name='1zgb/Align2/2'>active site. <scene name='1zgb/Align2/8'>Superposition of the <font color='cyan'>(R)-tacrine-(10)-hupyridone ((R)-3, cyan) and <font color='orange'>(S,S)-(-)-Bis(12)-hupyridone ((S,S)-(-)-4b, orange, i.e. 12-carbon-tether-linked hupyridone dimer) and <font color='plum'>(S,S)-(-)-Bis(10)-hupyridone ((S,S)-(-)-4a, plum) complexes demonstrates the binding mode of the hupyridone moiety. <font color='magenta'>TcAChE residues of symmetry-related molecule are shown in magenta. X-ray structures of TcAChE complexed with these 10- and 12-carbon-tether-linked 2 <scene name='1zgb/Align2/9'>dimers <font color='plum'>(S,S)-(-)-4a and <font color='orange'>(S,S)-(-)-4b show one moiety bound at the <scene name='1zgb/Align2/10'>CAS, the linker spanning the gorge, and the other moiety bound at the <scene name='1zgb/Align2/11'>PAS. There are two <scene name='1zgb/Align2/12'>hydrogen bonds connecting the <font color='cyan'>hupyridone <font color='red'>O to <font color='magenta'>Lys11 <font color='blue'>Nζ and <font color='cyan'>hupyridone <font color='blue'>N to <font color='magenta'>Gln185 <font color='red'>Oε1 of a <font color='magenta'>symmetry-related molecule in the <font color='cyan'>(R)-3 /TcAChE complex structure. <font color='red'>Water molecules are shown as red spheres. Another hydrogen bond connects the <font color='cyan'>hupyridone <font color='red'>O to a water molecule, which is bound to Ser286 N. Similarly, the hupyridone-PAS unit of both <font color='plum'>(-)-4a and <font color='orange'>(-)-4b forms direct and an water-mediated hydrogen bonds with the protein backbone in the PAS region.

</StructureSection>

About this Structure
1ZGB is a Single protein structure of sequence from Torpedo californica. Full crystallographic information is available from OCA.

Additional Resources
For additional information, see: Alzheimer's Disease

Reference
Crystal packing mediates enantioselective ligand recognition at the peripheral site of acetylcholinesterase., Haviv H, Wong DM, Greenblatt HM, Carlier PR, Pang YP, Silman I, Sussman JL, J Am Chem Soc. 2005 Aug 10;127(31):11029-36. PMID:16076210

Potent, easily synthesized huperzine A-tacrine hybrid acetylcholinesterase inhibitors., Carlier PR, Du DM, Han Y, Liu J, Pang YP, Bioorg Med Chem Lett. 1999 Aug 16;9(16):2335-8. PMID:10476864

Acetylcholinesterase complexed with bivalent ligands related to huperzine a: experimental evidence for species-dependent protein-ligand complementarity., Wong DM, Greenblatt HM, Dvir H, Carlier PR, Han YF, Pang YP, Silman I, Sussman JL, J Am Chem Soc. 2003 Jan 15;125(2):363-73. PMID:12517147

Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A., Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL, Nat Struct Biol. 1997 Jan;4(1):57-63. PMID:8989325

Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein., Sussman JL, Harel M, Frolow F, Oefner C, Goldman A, Toker L, Silman I, Science. 1991 Aug 23;253(5022):872-9. PMID:1678899

Page seeded by OCA on Mon Oct 20 12:03:50 2008